BlockInfo --------- The color distinction in the dot plot, the collinearity result and the Ks result are integrated into one file. This file contains the main information to achieve the purpose of easily screening the collinearity fragments. .. rubric:: Parameters .. tabularcolumns:: column spec ================ ======================================================================== Parameters Standards and instructions ---------------- ------------------------------------------------------------------------ collinearity Type: **file** | Default: **-** Colinearscan or MCScanX result file or gene pairs divided by tab. ---------------- ------------------------------------------------------------------------ score Type: **int** | Default: **100** Score value in the blast results. ---------------- ------------------------------------------------------------------------ evalue Type: **float** | Default: **1e-5** Evalue value in blast result. ---------------- ------------------------------------------------------------------------ repeat_number Type: **int** | Default: **10** The maximum number of homologous genes is allowed to remove more than part of the population. ---------------- ------------------------------------------------------------------------ position Type: {**order**} | Default: **order** The position of a gene corresponds to the gff file. ---------------- ------------------------------------------------------------------------ ks Type: **file** | Default: **-** Ks calculation results. ---------------- ------------------------------------------------------------------------ ks_col Type: **str** Default: **NG86** The result calculated by ks_YN00 or other methods is a single column. ---------------- ------------------------------------------------------------------------ savefile Type: **file** | Default: \* **.csv** Result file. ================ ======================================================================== Use command to enter the folder ``wgdi -bi ? >> total.conf`` Take out the parameter file. .. code-block:: python [blockinfo] blast = blast file gff1 = gff1 file gff2 = gff2 file lens1 = lens1 file lens2 = lens2 file collinearity = collinearity file score = 100 evalue = 1e-5 repeat_number = 10 position = order ks = ks file ks_col = ks_NG86 savefile = block information (*.csv) .. rubric:: Quick start After the parameters are modified properly, then run ``wgdi -bi total.conf`` .. rubric:: Example The original results are easily accessible at `wgdi-example `_ ================= ======================================================================== columns Information ----------------- ------------------------------------------------------------------------ id Type: **str** Unique id. ----------------- ------------------------------------------------------------------------ chr1,chr2 Type: **int** Two chromosomes corresponding to collinearity block. ----------------- ------------------------------------------------------------------------ start1,end1 Type: **int** The region of chromosome 1 on collinearity block. ----------------- ------------------------------------------------------------------------ start2,end2 Type: **int** The region of chromosome 2 on collinearity block. ----------------- ------------------------------------------------------------------------ pvalue Type: **float** Evaluate the compactness and uniqueness of collinear blocks, the range is 0-1, the better collinearity range is 0-0.2. ----------------- ------------------------------------------------------------------------ length Type: **int** The length of collinearity block. ----------------- ------------------------------------------------------------------------ ks_median Type: **float** The median of ks value on collinearity block. ----------------- ------------------------------------------------------------------------ ks_average Type: **float** The average of ks value on collinearity block. ----------------- ------------------------------------------------------------------------ homo1-5 Type: **float** The average of scores of different color dots (red=1, blue=0, gray=-1) on synteny blocks. ----------------- ------------------------------------------------------------------------ block1,block2 Type: **str** Gene pairs in collinear blocks ----------------- ------------------------------------------------------------------------ ks Type: **str** Output result of parameter `ks`. ----------------- ------------------------------------------------------------------------ tandem_ratio Type: **float** The density of tandem repeats, in general, a synteny block greater than 0.5 is unreliable. ----------------- ------------------------------------------------------------------------ density1,density2 Type: **float** Density of collinear blocks. ----------------- ------------------------------------------------------------------------ class1,class2 Type: **str** Class of collinear blocks. ================= ========================================================================